Sure! You only have to open the LevelEditor.cfg file (should be in your <Path to My documents folder>/HPL2/) with a text editor. Then add ExtraStaticObjectDir1="quoted full path to your custom static objects dir" for static objects, or ExtraEntityDir1="quoted full path to your custom entities dir" as an attribute in the "Directories" tag. If you have several directories, just increment the numeric suffix for each one.
A working example (ignore the LastUsedPath part):
<Directories LastUsedPath="D:/amnesia/redist/maps/main/ch01" ExtraEntityDir1="D:\HPL_2\redist\entities" />
Better if you move all new assets to the custom story root directory, cos right now the game will not look for them if they are outside it. If many model packs are made available to the public in a near future, we could look into making them shareable among custom stories
Also, when adding custom dirs, try to mimic how the game static_objects and entities folders are structured (as in 1 subfolder == 1 category). That will save the editor and yourself some headaches